Once MathJax is installed properly, the pretext/pretext script will be able to produce an EPUB version of your project. The script will first analyze your document, isolating all of the mathematics. These are then processed by MathJax and produce a file of representations of the mathematics, either as SVG images or as MathML versions. These representations are then inserted properly into the eventual output. This process is all automatic but explains why it is possible to produce two different types of EPUB. A good test of your installation is to use the pretext/pretext script to make an EPUB ([provisional cross-reference: epub production]) or the script can be used to simply produce structured files of these alternate representations (see [provisional cross-reference: script math representations] or paragraph just below).
With SRE also installed, text (speech) becomes a possible representation, as well as Nemeth braille. This makes possible an EPUB version that is all text, and there are online sites that will turn this EPUB into an audio book (of not very good quality). The braille representations are one component of the production of braille output. ([provisional cross-reference: braille production], Mathematics Representations)
If you use the pretext/pretext script with a math component, and a format of svg or mathml, you will produce a file of these representations, structured by XML (naturally). These files are not much use by themselves, but may be of interest.